[gmx-users] asking for help with dual-topology for TI

[Lei Zhou]

Dear gmx-users,

I am trying to set up a thermodynamic-integration to calculate the
free energy difference between two ligands. Both of them contains over
30 atoms and are quite different from each other.  I am wondering
whether GROMACS support dual-topology?  It is really a difficult job
for a beginner to setup the topology file for TI, especially in the
case of two very different ligands.

Can I just simply set all atoms in A to dummy atoms at lamda=1 and set
all atoms of B to dummy atoms at lamda=0?

Thank you.

Lei Zhou